On my server, we opted for the plugin "Regios" for area protection, as my admins and I have been using worldguard for a year or so now on our other servers and were kinda wanting to try something new. As far as we've noticed it has done it's job, it protects block placement and destruction, also seems to have easier control as far as flags go, and exceptions. If you haven't figured our your issue yet, i'd give it a try. We haven't had any problems with it at all.